Hi, both your code and the way you calculate VA using sire variance seems fine. In lmer residual variance is fixed as it assumes fixed relationship between variance and mean in binomial data so I'm not sure if simply putting this variance in your formula solves the problem. In MCMCglmm residual variance quantifies overdispersion so as far as I know here it's just a matter of substituting gaussian to multinomial2. Cheers, sz. -- Szymon Drobniak || Population Ecology Group Institute of Environmental Sciences,?Jagiellonian University ul. Gronostajowa 7, 30-387 Krak?w, POLAND tel.: +48 12 664 51 79 fax: +48 12 664 69 12 www.eko.uj.edu.pl/drobniak
animal model: calculating heritability and evolvability from sire effects
2 messages · Szymek Drobniak, Pierre de Villemereuil
Hi ! Concerning the 4 coefficient : you say the additive variance is estimated within the full-sibs of the same sire. Is that to say offspring of the same sire descent as well from the same dam ? In that case (same father and same mother), then the relationship coefficient is of 1/2 (2 * coefficient of coancestry of 1/4). So, I think (but I can be wrong) the coefficient should be 2. If each individual descent from a different mother, then kinship is 1/4. So the coefficient of 4 is correct. When estimating the heritability of a binomial trait, you have to keep the residual variance in the total variance. Just add the 'link variance' (say Vlink) such as : h? = Va / (Va + Vr + Vlink) (Vlink is pi?/3 for logit link and 1 for probit link) Cheers, Pierre. Le 21/12/2011 12:18, Szymek Drobniak a ?crit :
Hi, both your code and the way you calculate VA using sire variance seems fine. In lmer residual variance is fixed as it assumes fixed relationship between variance and mean in binomial data so I'm not sure if simply putting this variance in your formula solves the problem. In MCMCglmm residual variance quantifies overdispersion so as far as I know here it's just a matter of substituting gaussian to multinomial2. Cheers, sz. -- Szymon Drobniak || Population Ecology Group Institute of Environmental Sciences, Jagiellonian University ul. Gronostajowa 7, 30-387 Krak?w, POLAND tel.: +48 12 664 51 79 fax: +48 12 664 69 12 www.eko.uj.edu.pl/drobniak
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